[Chimera-users] New residues for swap commands

[Rodrigo Galindo-Murillo]

Thank you both for your suggestions. I already have a decent amount of
new residues parameterized for AMBER (topo/coord files) and I was
looking for a way to randomly swap those into a peptide.

Best,
Rodrigo

On Wed, Jun 15, 2022 at 12:33 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Elaine's ideas are definitely the most practical.  It is possible to add additional residue swap types to Chimera, but I'd say it's somewhat difficult if you are pretty familiar with Python, and crazy hard if you aren't that familiar with Python.  The approach would also depend on whether you were actually adding rotamers or just one conformation per residue type.  Anyway, if you are a Pythonista and Elaine's recommendations don't cover your needs, I can offer some guidance on what's needed.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On Jun 15, 2022, at 11:07 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Rodrigo,
> It may be difficult to add your own, since it could involve understanding the code and defining multiple rotamers (conformations) of each side chain.  The swap commands are especially useful because they help choose among the multiple rotamers.  However, here are some other suggestions:
>
> (1) If you get the SwissSidechain plugin for Chimera,
> <https://swisssidechain.ch/visualization/chimera.php>
>
> ... it will allow using a different command "swapnaa" (non-natural amino acids) to substitute any of >200 non-natural amino acids that are in the SwissSidechain database:
> <https://www.swisssidechain.ch/>
>
> Browse that database to see what it includes:
> <https://swisssidechain.ch/browse.php>
>
> I'm not aware of any similar capability for nucleotides, however.
>
> (2) if the new residue is similar to a standard residue or one available in the database above (e.g. you just need to add a methyl group or other small substituent, or change the element of an atom), it would be simpler just to change that residue one atom at a time in Chimera with the Build Structure tool (in menu under Tools.. Structure Editing), the Modify Structure section:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#modify>
>
> (3) yet another possibility is if you have a PDB file that contains the nonstandard residue, you could match its backbone onto the position that you want to modify in the original, then save that PDB file relative to the original model, then manually text-edit a copy of the original model PDB file to substitute in the coordinates of the nonstandard residue from the PDB file you just saved.  You might need to do some other things like edit residue number and chain.  This is not too bad if you are rather familiar with PDB format..
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> On Jun 15, 2022, at 10:19 AM, Rodrigo Galindo-Murillo via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hello!
> Is it possible to add new amino acids to the swapaa and new
> nucleotides for the swapna commands?
>
> Thank you!
> Rodrigo.
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
>
>